An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data

Abstract

Background: Protein-protein interactions (PPIs) are challenging but attractive targets for small chemical drugs. Whole PPIs, called the 'interactome', have been emerged in several organisms, including human, based on the recent development of high-throughput screening (HTS) technologies. Individual PPIs have been targeted by small drug-like chemicals (SDCs), however, interactome data have not been fully utilized for exploring drug targets due to the lack of comprehensive methodology for utilizing these data. Here we propose an integrative in silico approach for discovering candidates for drug-targetable PPIs in interactome data.

Results: Our novel in silico screening system comprises three independent assessment procedures: i) detection of protein domains responsible for PPIs, ii) finding SDC-binding pockets on protein surfaces, and iii) evaluating similarities in the assignment of Gene Ontology (GO) terms between specific partner proteins. We discovered six candidates for drug-targetable PPIs by applying our in silico approach to original human PPI data composed of 770 binary interactions produced by our HTS yeast two-hybrid (HTS-Y2H) assays. Among them, we further examined two candidates, RXRA/NRIP1 and CDK2/CDKN1A, with respect to their biological roles, PPI network around each candidate, and tertiary structures of the interacting domains.

Conclusion: An integrative in silico approach for discovering candidates for drug-targetable PPIs was applied to original human PPIs data. The system excludes false positive interactions and selects reliable PPIs as drug targets. Its effectiveness was demonstrated by the discovery of the six promising candidate target PPIs. Inhibition or stabilization of the two interactions may have potential therapeutic effects against human diseases.

Figure 1

Schematic representation of our novel and integrative in silico system for discovering candidates for drug-targetable PPIs in binary PPI data. The system uses binary PPI data as an input and assesses each PPI based on three independent in silico investigations; detection of protein domains responsible for PPIs, finding SDC-binding pockets on protein surfaces, and evaluating similarities in the assignment of GO terms. By integrating the results of these three investigations, the system discovers candidates for drug-targetable PPIs.

Figure 2

Selecting candidates for drug-targetable PPIs. Numbers of the bait-prey pairs satisfying one, two, or three criteria are shown in each region. Nine bait-prey pairs satisfy all the three criteria.

Figure 3

PPI network connecting proteins used in the HTS-Y2H assays in the present study. Part of the network around the RXRA/NRIP1 and CDK2/CDKN1A interactions is enlarged in the upper frame. Proteins are represented as diamonds (targets of drugs approved by FDA) and circles (non-targets of FDA-approved drugs). The information on target proteins of FDA-approved drugs was obtained from the DrugBank database [58]. RXRA, NRIP1, CDK2, and CDKN1A are colored yellow. Proteins related to OMIM [96] diseases are colored brown and the remaining proteins are grey. Interactions between proteins are indicated by lines. Novel PPIs detected in this study are shown in red, and those retrieved form a public database, HPRD [57], are in blue. PPIs are colored green if the interaction was detected in the present study and also retrieved from the HPRD. The network was drawn using the program Cytoscape (version 2.3.2) [97]. See Additional file 4 for the original and larger version of the PPI network.

Figure 4

Locations of the detected pockets superimposed on the tertiary structures of proteins or the amino acid sequence. (a) The main chain of Hormone_recep domain of RXRA [PDB:1MVC_A] is shown by a ribbon model and is colored grey. Atoms of the four detected pockets are shown as space-filling models, and each pocket is colored green (1,092ų, 64%), blue (463ų, 48%), light blue (169ų, 82%), or yellow (152ų, 78%), (the volume and the hydrophobic residue ratio of each pocket are shown in parentheses). The H12 region is shown in red. (b) Amino acid sequence of the Hormone_recep domain of RXRA [PDB:1MVC_A]. Amino acid residues comprising each pocket are color-coded as in (a). (c) Location of a pocket laid across CDK2 and CDKN1B on CDK2/CDKN1B/cyclin A complex [PDB:1JSU]. CDK2, CDKN1B, and cyclin A are shown in green, magenta, and grey, respectively. Atoms are colored blue composing of the pocket with the size of 714ų and the hydrophobic residue ratio of 50%. The location of the 'cyclin groove' [62] already studied as drug target is also shown. The figures were drawn using the CASTp [39].